EP3425066A1 - Déterminations de cancer du poumon à l'aide d'arnmi - Google Patents

Déterminations de cancer du poumon à l'aide d'arnmi Download PDF

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EP3425066A1
EP3425066A1 EP18175641.2A EP18175641A EP3425066A1 EP 3425066 A1 EP3425066 A1 EP 3425066A1 EP 18175641 A EP18175641 A EP 18175641A EP 3425066 A1 EP3425066 A1 EP 3425066A1
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mir
hsa
mirna
expression
ratios
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Gabriella Sozzi
Mattia BOERI
Ugo PASTORINO
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BioMirna Holdings Ltd
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BioMirna Holdings Ltd
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/6813—Hybridisation assays
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    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays
    • C—CHEMISTRY; METALLURGY
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    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA

Definitions

  • the present application generally relates to diagnosis and determining risk of lung cancer. More specifically, the application is directed to the use of miRNA expression ratios to determine a risk for manifesting a pulmonary tumor or an aggressive pulmonary tumor, and for determining the presence of a pulmonary tumor or an aggressive pulmonary tumor.
  • Lung cancer is the leading cause of cancer death worldwide ( Jemal et al., CA Cancer J Clin, 61:69-9, 2011 ). Currently the majority of lung cancers are detected at an advanced stage where treatments have limited efficacy and survival rates are low. Detection of lung cancer at an early stage may significantly reduce mortality.
  • the present invention is based in part on the discovery that assay methods may utilize circulating miRNA biomarkers to provide a three-level classifier for an overall "risk of developing or having a pulmonary tumor" assay.
  • a method of determining the presence of a pulmonary tumor in a subject comprises:
  • a method of determining the presence of an aggressive pulmonary tumor in a subject comprises:
  • a method of determining the risk of manifesting a pulmonary tumor in a subject comprises:
  • a method of determining the risk of manifesting an aggressive pulmonary tumor comprises:
  • a method for predicting the risk of developing or having a pulmonary tumor in a subject comprises:
  • a method of establishing treatment options for a subject comprises testing the subject using any of the above methods, and determining treatment options according to the results of the method.
  • the method may further comprise administering a treatment to the subject in need of such treatment.
  • the present invention utilizes multiple ratios of miRNA expression levels to determine (a) the risk of manifesting a pulmonary tumor, (b) the risk of manifesting an aggressive pulmonary tumor, (c) the presence of a pulmonary tumor, (d) the presence of an aggressive tumor, and, when combining the risk detected in steps (a)-(d), determining the overall risk of having or developing a pulmonary tumor.
  • the present invention may include elimination of samples having detectable levels of hemolysis, e.g., by including the use of a miRNA hemolysis classifier; use of a three-level (Low, Intermediate or High) "risk of disease” classifier instead of a two-level (Low, High) classifier; or the use of control plasma samples from single subjects, instead of pools.
  • Three miRNAs may be included, miR-101, miR-145 and miR-133a, which were excluded in the validation step of previous assays because of high variability in the control pools.
  • the "microRNA signature classifier” provides a screening sensitivity of 87% for MSC alone and 98% when combined with low-dose computed tomography (LDCT) screening Accordingly, the MSC can be used separately or in combination with other methods, such as LDCT, in a synergistic approach to improve the effectiveness of LDCT for lung cancer screening by avoiding further rounds of LDCTs in a large proportion of subjects and unnecessary invasive diagnostic follow-up.
  • LDCT low-dose computed tomography
  • MSC The development of MSC was based on a non-biased computational approach of screening 4,950 ratios of 100 different plasma miRNAs for the selection of the optimal set of miRNA ratios for lung cancer detection and association with poor prognosis ( Boeri et al., Proc Natl Acad Sci USA 108:3713-3718, 2011 ). These miRNA ratios may reflect regulation between competing mechanisms of miRNA regulation of miRNAs within different cellular components of the tumor and the surrounding microenvironment.
  • stromal cells may be activated by the inflamed lung microenvironment, releasing specific miRNAs into the circulation that could be functionally engaged in the regulation of target genes associated with neoplastic transformation.
  • the MSC utilizes a robust assay of plasma-derived miRNA signatures.
  • the MSC has diagnostic performance for malignant disease presence, risk of future malignancy and ability to distinguish lung cancers from the large majority of benign LDCT-detected pulmonary nodules.
  • the particular signatures which may be utilized by the MSC are detailed herein.
  • a method of determining the presence of a pulmonary tumor in a subject comprises:
  • the miRNA pairs of this assay comprise more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, more than 10, more than 11, more than 12, or each of the ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, and 320/660, or the inverse ratios thereof.
  • the miRNA pairs can further comprise the ratios 106a/660, 106a/92a, 126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660, 17/92a, 197/660, 197/92a, 19b/660, or 28-3p/660, or the inverse ratios thereof.
  • the miRNA pairs comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, 320/660, 106a/660, 106a/92a, 126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660, 17/92a, 197/660, 197/92a, 19b/660, and 28-3p/660, or the inverse
  • the invention provides the use of a plurality of primers or probes useful for detecting any of 27 miRNA pairs in the manufacture of a diagnostic reagent useful in determining the presence of a pulmonary tumor in a subject, wherein the detection comprises:
  • the plurality of primers or probes are useful for detecting more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, more than 10, more than 11, more than 12, or each of the miRNA pair expression ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, and 320/660, or the inverse ratios thereof.
  • the plurality of primers or probes are further useful for detecting the miRNA pair expression ratios 106a/660, 106a/92a, 126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660, 17/92a, 197/660, 197/92a, 19b/660, or 28-3p/660, or the inverse ratios thereof.
  • the plurality of primers or probes are useful for detecting at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, 320/660, 106a/660, 106a/92a, 126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660, 17/92a, 197/660, 197/92a, 19b/
  • At least one primer or probe in the plurality of primers and probes is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes comprises at least one primer or probe capable of selectively binding to at least one miRNA of at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, 320/660, 106a/660, 106a/92a, 126/660, 140-5p
  • the invention provides a kit for determining the presence of a pulmonary tumor in a subject.
  • the kit comprises a plurality of primers or probes useful for detecting any of 27 miRNA pairs in the manufacture of a diagnostic reagent and instructions for determining the presence of a pulmonary tumor in a subject utilizing the plurality of primers or probes.
  • the instructions comprise:
  • the plurality of primers or probes provided in the kit are useful for detecting more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, more than 10, more than 11, more than 12, or each of the miRNA pair expression ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, and 320/660, or the inverse ratios thereof.
  • the plurality of primers or probes provided in the kit are further useful for detecting the miRNA pair expression ratios 106a/660, 106a/92a, 126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660, 17/92a, 197/660, 197/92a, 19b/660, or 28-3p/660, or the inverse ratios thereof.
  • the plurality of primers or probes provided in the kit are useful for detecting at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, 320/660, 106a/660, 106a/92a, 126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660, 17/92a, 197/660, 197/92a, 197/660
  • At least one primer or probe in the plurality of primers and probes provided in the kit is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes provided in the kit comprises at least one primer or probe capable of selectively binding to at least one miRNA of at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, 320/660, 106a/660, 106a/92a,
  • a method of determining the presence of an aggressive pulmonary tumor in a subject comprises:
  • the miRNA pairs of this assay comprise more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, or each of the ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, and 320/660, or the inverse ratios thereof.
  • the miRNA pairs can further comprise the ratios 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660, 197/92a, 19b/451, 19b/486-5p, 19b/660, 28-3p/451, or 28-3p/486-5p, or the inverse ratios thereof.
  • the miRNA pairs comprise at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, 320/660, 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660, 197/92a, 19b/451, 19b/486-5p, 19b/660, 28-3p/451, or 28-3p/486-5p, or the inverse ratios thereof.
  • the skilled artisan would understand that utilizing some but not all of these 28 ratios would be expected to provide an assay that accurately identifies
  • the invention provides the use of a plurality of primers or probes useful for detecting any of 28 miRNA pairs in the manufacture of a diagnostic reagent useful in determining the presence of an aggressive pulmonary tumor in a subject, wherein the detection comprises:
  • the plurality of primers or probes are useful for detecting more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, or each of the miRNA pair expression ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, and 320/660, or the inverse ratios thereof.
  • the plurality of primers or probes are further useful for detecting the miRNA pair expression ratios 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660, 197/92a, 19b/451, 19b/486-5p, 19b/660, 28-3p/451, or 28-3p/486-5p, or the inverse ratios thereof.
  • the plurality of primers or probes are useful for detecting at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the miRNA pair expression ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, 320/660, 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660, 197/92a, 19b/451, 19b/486-5p, 19b/660, 28-3p/451, or 28-3p/486-5p, or the inverse ratios thereof.
  • the skilled artisan would understand that utilizing some but not all of these 28 ratios
  • At least one primer or probe in the plurality of primers and probes is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes comprises at least one primer or probe capable of selectively binding to at least one miRNA of at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the miRNA pair expression ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, 320/660, 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660, 197/92a, 19
  • the invention provides a kit for determining the presence of an aggressive pulmonary tumor in a subject.
  • the kit comprises a plurality of primers or probes useful for detecting any of 28 miRNA pairs in the manufacture of a diagnostic reagent and instructions for determining the presence of an aggressive pulmonary tumor in a subject utilizing the plurality of primers or probes.
  • the instructions comprise:
  • the plurality of primers or probes are useful for detecting more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, or each of the miRNA pair expression ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, and 320/660, or the inverse ratios thereof.
  • the plurality of primers or probes are further useful for detecting the miRNA pair expression ratios 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660, 197/92a, 19b/451, 19b/486-5p, 19b/660, 28-3p/451, or 28-3p/486-5p, or the inverse ratios thereof.
  • the plurality of primers or probes are useful for detecting at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the miRNA pair expression ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, 320/660, 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660, 197/92a, 19b/451, 19b/486-5p, 19b/660, 28-3p/451, or 28-3p/486-5p, or the inverse ratios thereof.
  • At least one primer or probe in the plurality of primers and probes provided in the kit is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes provided in the kit comprises at least one primer or probe capable of selectively binding to at least one miRNA of at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the miRNA pair expression ratios 106a/16, 106/660, 16/17, 16/320, 17/660, 197/30b, 197/30c, 320/451, 320/486-5p, 320/660, 106a/451, 106a/486-5p, 126/451, 126/486-5p, 126/660, 140-5p/197, 16/197, 17/451, 17/486-5p, 197/451, 197/486-5p, 197/660/660
  • prognostic signatures are provided - a "risk of manifesting a pulmonary tumor” signature, and a “risk of manifesting an aggressive pulmonary tumor” signature. These prognostic signatures can be utilized for determining risk within any time period after the sample is taken, e.g., 3 months, 6 months, 12 months, 18 months, 24 months, 36 months, or any time outside or in-between those time periods.
  • a method of determining the risk of manifesting a pulmonary tumor in a subject comprises:
  • the miRNA pairs of this assay comprise more than 2, more than 3, more than 4, more than 5, or each of the ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, and 28-3p/451, or the inverse ratios thereof.
  • the miRNA pairs can further comprise the ratios 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/92a, 197/19b, 197/451, 197/660, 197/92a, 19b/660, 28-3p/660, or 320/660, or the inverse ratios thereof.
  • the miRNA pairs comprise at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, 28-3p/451, 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/92a, 197/19b, 197/451, 197/660, 197/92a, 19b/660, 28-3p/660, or 320/660, or the inverse ratios thereof.
  • the skilled artisan would understand that utilizing some but not all of these 27 ratios would be expected to provide an assay that accurately
  • the invention provides the use of a plurality of primers or probes useful for detecting any of 27 miRNA pairs in the manufacture of a diagnostic or prognostic reagent useful in determining the risk of manifesting a pulmonary tumor in a subject, wherein the detection comprises:
  • the plurality of primers or probes are useful for detecting more than 2, more than 3, more than 4, more than 5, or each of the miRNA pair expression ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, and 28-3p/451, or the inverse ratios thereof.
  • the plurality of primers or probes are further useful for detecting the miRNA pair expression ratios 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/92a, 197/19b, 197/451, 197/660, 197/92a, 19b/660, 28-3p/660, or 320/660, or the inverse ratios thereof.
  • the plurality of primers or probes are useful for detecting at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, 28-3p/451, 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/92a, 197/19b, 197/451, 197/660, 197/92a, 19b/660, 28-3p/660, or 320/660, or the inverse ratios thereof.
  • the skilled artisan would understand that utilizing some but not all of these 27
  • At least one primer or probe in the plurality of primers and probes is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes comprises at least one primer or probe capable of selectively binding to at least one miRNA of at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, 28-3p/451, 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/92a, 197/19b,
  • the invention provides a kit for determining the risk of manifesting a pulmonary tumor in a subject.
  • the kit comprises a plurality of primers or probes useful for detecting any of 27 miRNA pairs in the manufacture of a diagnostic or prognostic reagent and instructions for determining the risk of manifesting a pulmonary tumor in a subject utilizing the plurality of primers or probes.
  • the instructions comprise:
  • the plurality of primers or probes are useful for detecting more than 2, more than 3, more than 4, more than 5, or each of the miRNA pair expression ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, and 28-3p/451, or the inverse ratios thereof.
  • the plurality of primers or probes are further useful for detecting the miRNA pair expression ratios 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/92a, 197/19b, 197/451, 197/660, 197/92a, 19b/660, 28-3p/660, or 320/660, or the inverse ratios thereof.
  • the plurality of primers or probes are useful for detecting at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, 28-3p/451, 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/92a, 197/19b, 197/451, 197/660, 197/92a, 19b/660, 28-3p/660, or 320/660, or the inverse ratios thereof.
  • At least one primer or probe in the plurality of primers and probes provided in the kit is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes provided in the kit comprises at least one primer or probe capable of selectively binding to at least one miRNA of at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or each of the miRNA pair expression ratios 133a/92a, 15b/21, 15b/30b, 15b/30c, 16/197, 28-3p/451, 101/140-3p, 106a/451, 106a/660, 106a/92a, 126/660, 133a/451, 133a/660, 140-3p/660, 142-3p/15b, 15b/451, 15b/660, 17/451, 17/660, 17/
  • a method of determining the risk of manifesting an aggressive pulmonary tumor in a subject comprises:
  • the miRNA pairs of this assay comprise more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, or each of the ratios 106a/142-3p, 126/142-3p, 126/21, 126/92a, 142-3p/17, 142-3p/197, 142-3p/28-3p, 197/19b, 197/660, and 28-3p/660, or the inverse ratios thereof.
  • the miRNA pairs can further comprise the ratios 106a/451, 126/451, 145/197, 17/451, 197/21, 197/30b, 197/30c, 197/451, 197/92a, 19b/451, 21/221, 21/28-3p, 28-3p/30b, 28-3p/30c, 28-3p/451, 28-3p/92a, 320/451, or 320/92a, or the inverse ratios thereof.
  • the miRNA pairs comprise at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the ratios 106a/142-3p, 126/142-3p, 126/21, 126/92a, 142-3p/17, 142-3p/197, 142-3p/28-3p, 197/19b, 197/660, 28-3p/660, 106a/451, 126/451, 145/197, 17/451, 197/21, 197/30b, 197/30c, 197/451, 197/92a, 19b/451, 21/221, 21/28-3p, 28-3p/30b, 28-3p/30c, 28-3p/451, 28-3p/92a, 320/451, and 320/92a, or the inverse ratios thereof.
  • the skilled artisan would understand that utilizing some but not all of these 28 ratios would be expected
  • the invention provides the use of a plurality of primers or probes useful for detecting any of 28 miRNA pairs in the manufacture of a diagnostic or prognostic reagent useful in determining the risk of manifesting an aggressive pulmonary tumor in a subject, wherein the detection comprises:
  • the plurality of primers or probes are useful for detecting more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, or each of the miRNA pair expression ratios 106a/142-3p, 126/142-3p, 126/21, 126/92a, 142-3p/17, 142-3p/197, 142-3p/28-3p, 197/19b, 197/660, and 28-3p/660, or the inverse ratios thereof.
  • the plurality of primers or probes are further useful for detecting the miRNA pair expression ratios 106a/451, 126/451, 145/197, 17/451, 197/21, 197/30b, 197/30c, 197/451, 197/92a, 19b/451, 21/221, 21/28-3p, 28-3p/30b, 28-3p/30c, 28-3p/451, 28-3p/92a, 320/451, or 320/92a, or the inverse ratios thereof.
  • the plurality of primers or probes are useful for detecting at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the miRNA pair expression ratios 106a/142-3p, 126/142-3p, 126/21, 126/92a, 142-3p/17, 142-3p/197, 142-3p/28-3p, 197/19b, 197/660, 28-3p/660, 106a/451, 126/451, 145/197, 17/451, 197/21, 197/30b, 197/30c, 197/451, 197/92a, 19b/451, 21/221, 21/28-3p, 28-3p/30b, 28-3p/30c, 28-3p/451, 28-3p/92a, 320/451, and 320/92a, or the inverse ratios thereof.
  • the skilled artisan would understand that
  • the invention provides a kit for determining the risk of manifesting an aggressive pulmonary tumor in a subject.
  • the kit comprises a plurality of primers or probes useful for detecting any of 28 miRNA pairs in the manufacture of a diagnostic or prognostic reagent and instructions for determining the risk of manifesting an aggressive pulmonary tumor in a subject utilizing the plurality of primers or probes.
  • the instructions comprise:
  • the plurality of primers or probes are useful for detecting more than 2, more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, or each of the miRNA pair expression ratios 106a/142-3p, 126/142-3p, 126/21, 126/92a, 142-3p/17, 142-3p/197, 142-3p/28-3p, 197/19b, 197/660, and 28-3p/660, or the inverse ratios thereof.
  • the plurality of primers or probes are further useful for detecting the miRNA pair expression ratios 106a/451, 126/451, 145/197, 17/451, 197/21, 197/30b, 197/30c, 197/451, 197/92a, 19b/451, 21/221, 21/28-3p, 28-3p/30b, 28-3p/30c, 28-3p/451, 28-3p/92a, 320/451, or 320/92a, or the inverse ratios thereof.
  • the plurality of primers or probes are useful for detecting at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the miRNA pair expression ratios 106a/142-3p, 126/142-3p, 126/21, 126/92a, 142-3p/17, 142-3p/197, 142-3p/28-3p, 197/19b, 197/660, 28-3p/660, 106a/451, 126/451, 145/197, 17/451, 197/21, 197/30b, 197/30c, 197/451, 197/92a, 19b/451, 21/221, 21/28-3p, 28-3p/30b, 28-3p/30c, 28-3p/451, 28-3p/92a, 320/451, and 320/92a, or the inverse ratios thereof.
  • At least one primer or probe in the plurality of primers and probes provided in the kit is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes provided in the kit comprises at least one primer or probe capable of selectively binding to at least one miRNA of at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or each of the miRNA pair expression ratios 106a/142-3p, 126/142-3p, 126/21, 126/92a, 142-3p/17, 142-3p/197, 142-3p/28-3p, 197/19b, 197/660, 28-3p/660, 106a/451, 126/451, 145/197, 17/451, 197/21, 197/30b, 197/30c, 197/451, 197/92a, 19b/451,
  • That method comprises:
  • That use comprises:
  • pulmonary tumor a used herein can be either a benign or malignant pulmonary tumor.
  • the pulmonary tumor can be associated with one or more lung conditions and may take the form of, e.g., a pulmonary nodule or a pulmonary mass.
  • lung condition refers to a disease, event, or change in health status relating to the lung, including for example lung cancer and various non-cancerous conditions.
  • non-cancerous lung condition include chronic obstructive pulmonary disease (COPD), benign pulmonary tumors or masses of cells (e.g., hamartoma, fibroma, neurofibroma), granuloma, sarcoidosis, and infections caused by bacterial (e.g., tuberculosis) or fungal (e.g., histoplasmosis) pathogens.
  • COPD chronic obstructive pulmonary disease
  • benign pulmonary tumors or masses of cells e.g., hamartoma, fibroma, neurofibroma
  • granuloma e.g., sarcoidosis
  • lung cancer preferably refers to cancers of the lung, but may include any disease or other disorder of the respiratory system of a human or other mammal.
  • Respiratory neoplastic disorders include, for example small cell carcinoma or small cell lung cancer (SCLC), non-small cell carcinoma or non-small cell lung cancer (NSCLC), squamous cell carcinoma (SCC), adenocarcinoma, broncho-alveolar carcinoma (BAC), mixed pulmonary carcinoma, malignant pleural mesothelioma, undifferentiated large cell carcinoma, giant cell carcinoma, synchronous tumors, large cell neuroendocrine carcinoma, adenosquamous carcinoma, undifferentiated carcinoma; and small cell carcinoma, including oat cell cancer, mixed small cell/large cell carcinoma (LC), large cell carcinoma, and combined small cell carcinoma; as well as adenoid cystic carcinoma, hamartomas, mucoepidermoid tumors, typical carcinoid lung tumors, atypical carcinoid lung tumors, peripheral carcinoid lung tumors, central carcinoid lung tumors, pleural mesotheliomas, undifferentiated pulmonary carcinoma and cancers that originate
  • biological sample from the subject refers to a sample from any subject, including smokers, non-smokers, former smokers, cancer patients (e.g., for diagnosing and/or monitoring cancer recurrence after treatment), former cancer patients, etc.
  • the biological sample originates from a smoker individual who, at the moment of the collection of the sample, does not present a pulmonary tumor if subjected to imaging diagnostic methods, in particular the smoker individual not presenting nodules of dimensions of greater than 5 mm if subjected to a spiral CT scan.
  • biological sample can be any tissue that provides an accurate measurement of the miRNA profile in the subject.
  • the biological sample is a biological fluid.
  • these embodiments are not narrowly limited to any particular bodily fluid, since miRNA is present in essentially all bodily fluids ( Weber et al., The microRNA spectrum in 12 body fluids, Clin Chem 56:1733-1741, 2010 ; De Guire et al., Clin Biochem 46:846-860, 2013 ; see also Rodriguez-Dorantes et al., Meth Mol Biol 1165:81-87, 2014 ).
  • bodily fluids are peripheral blood, serum, plasma, ascites, urine, sputum, saliva, broncheoalveolar lavage fluid, cyst fluid, pleural fluid, peritoneal fluid, lymph, pus, lavage fluids from sinus cavities, bronchopulmonary aspirates, and bone marrow aspirates.
  • the bodily fluid is plasma or serum.
  • the biological sample is a tissue sample.
  • an "individual”, “subject”, “patient” or “subject in need thereof” is an individual having an risk of developing a tumor or an aggressive tumor or one who may have or may be afflicted with, or diagnosed as having, a tumor or aggressive tumor. These terms may be utilized interchangeably.
  • the individual is a mammal.
  • the mammal can be e.g., any mammal, e.g., a human, primate, bird, mouse, rat, fowl, dog, cat, cow, horse, goat, camel, sheep or a pig.
  • the mammal is a human.
  • a "primer” or a “probe” in the plurality of primers or probes is a nucleic acid molecule.
  • the primer or probe can be DNA, RNA, or cDNA.
  • the primer or probe can be naturally occurring or synthetic.
  • the primer or probe can be at least 5, at least 10, at least 15, at least 20, at least 25, at least 50, at least 75, at least 100 nucleic acids in length.
  • at least one primer or probe in the plurality of primers and probes is capable of selectively binding to at least one miRNA of a miRNA pair in a sample.
  • the plurality of primers or probes comprises at least one primer or probe capable of selectively binding to at least one miRNA of all the miRNA pair expression rations in a sample.
  • selectively binding means that the primer or probe has a high affinity for binding to at least one miRNA of a miRNA pair in a sample or a higher affinity for binding to at least one miRNA of a miRNA pair as compared to any other miRNA in a sample.
  • primer means that the nucleic acid molecule is capable of serving as a starting point for DNA synthesis. That is, DNA polymerases can initiate replication from the 3' end of a primer.
  • the term "the expression ratio of an miRNA pair" as used herein is the ratio of the expression level of two specific miRNAs. It should be appreciated that the ratios for any of the miRNA pairs specified in any of the methods described herein could be calculated as the inverse ratio of that specified.
  • the miRNA pairs for a particular method are "106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221, 142-3p/30b, and 320/660, or the inverse ratios thereof," the expression ratio of any one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or thirteen of these miRNA pairs could be calculated as the inverse ratio, where the cut-off values are adjusted accordingly.
  • cut-off value can be a negative or a positive number.
  • an expression ratio that "exceeds the cut-off value” is a value that is lesser in magnitude than the cut-off value.
  • an expression ratio that "exceeds the cut-off value” is a value that is greater in magnitude than the cut-off value. See, e.g., Table 9, where ">" indicates that a number greater in magnitude than the cut-off value signifies a ratio that exceeds the cut-off, and " ⁇ " indicate that a number lesser in magnitude than the cut-off value signifies a ratio that exceeds the cut-off value.
  • the cut-off value for the expression ratio of any particular miRNA pair is determined from the average ratio of a plurality of corresponding miRNA pairs from a plurality of control samples.
  • the term "plurality of control samples" as used herein can be from any defined population, for example healthy subjects without a history of any cancer, healthy subjects without a history of lung cancer, subjects that have lung cancer, subjects that never smoked, subjects that have smoked but no longer smoke, etc.
  • the plurality of control samples are from healthy subjects and the cut-off value is the average ratio of the plurality of corresponding miRNA pairs from the plurality of control samples.
  • the term "average” as used herein can be the mean or median.
  • the cut-off is the average +/- one standard deviation, or any smaller or larger proportion of the standard deviation, for example +/- 1 ⁇ 2 standard deviation, +/- 3 ⁇ 4 standard deviation, +/- 1.5 standard deviations, +/- 2 standard deviations, or any larger, smaller, or in-between proportion of the standard deviation.
  • the cut-off value can be determined without undue experimentation for any plurality of control samples from any control population by using known methods, for example by using training sets, as described in the Examples.
  • the cut-off is established to achieve the sensitivity (SE), specificity (SP), positive predictive value (PPV) and negative predictive value (NPV) desired.
  • the diagnostic or prognostic value of the methods can be defined by its SE, SP, PPV and NPV. Any test method will produce True Positive (TP), False Negative (FN), False Positive (FP), and True Negative (TN).
  • TP True Positive
  • FN False Negative
  • FP False Positive
  • TN True Negative
  • the "sensitivity" of a test is the percentage of all patients with disease present or that do respond who have a positive test or (TP/TP+FN) ⁇ 100%.
  • the "specificity” of a test is the percentage of all patients without disease or who do not respond, who have a negative test or (TN/FP+TN) ⁇ 100%.
  • the "predictive value” or “PV” of a test is a measure (%) of the times that the value (positive or negative) is the true value, i.e., the percent of all positive tests that are true positives is the Positive Predictive Value (PV+) or (TP/TP+FP)x100%.
  • the "negative predictive value” (PV) is the percentage of patients with a negative test who will not respond or (TN/FN+TN) ⁇ 100%.
  • the "accuracy” or “efficiency” of a test is the percentage of the times that the test give the correct answer compared to the total number of tests or (TP+TN/TP+TN+FP+FN) ⁇ 100%.
  • the "error rate” calculates from those patients predicted to respond who did not and those patients who responded that were not predicted to respond or (FP+FN/TP+TN+FP+FN) ⁇ 100%.
  • the overall test "specificity” is a measure of the accuracy of the sensitivity and specificity of a test do not change as the overall likelihood of disease changes in a population, the predictive value does change.
  • the TP, FN, FP and TN can be determined and adjusted by the skilled artisan without undue experimentation by, e.g., adjusting the cut-off value, adjusting the statistical significance (e.g., the P value) for making a prognostic or diagnostic determination; adjusting the accuracy of the test procedures, etc.
  • the expression levels of the miRNAs can be determined by any means known in the art. In some embodiments, the expression levels are determined by making cDNA copies of each miRNA in each miRNA pair using reverse transcriptase-polymerase chain reaction (RT-PCR). In various embodiments, the expression ratio is further determined using real time PCR. In specific embodiments of these methods, the expression ratio is further determined using TaqMan probes. However, the methods are not limited to those embodiments and may be practiced using any appropriate method now known or later discovered for determining miRNA expression levels.
  • RT-PCR reverse transcriptase-polymerase chain reaction
  • the miRNA is amplified prior to measurement. In other embodiments, the level of those nucleic acids is measured during the amplification process. In still other methods, the nucleic acids are not amplified prior to measurement.
  • nucleic acid polymerization and amplification techniques include reverse transcription (RT), polymerase chain reaction (PCR), real-time PCR (quantitative PCR (q-PCR)), nucleic acid sequence-base amplification (NASBA), ligase chain reaction, multiplex ligateable probe amplification, invader technology (Third Wave), rolling circle amplification, in vitro transcription (IVT), strand displacement amplification, transcription-mediated amplification (TMA), RNA (Eberwine) amplification, and other methods that are known to persons skilled in the art.
  • RT reverse transcription
  • PCR polymerase chain reaction
  • q-PCR quantitative PCR
  • NASBA nucleic acid sequence-base amplification
  • ligase chain reaction multiplex ligateable probe amplification
  • IVT in vitro transcription
  • TMA transcription-mediated amplification
  • RNA (Eberwine) amplification and other methods that are known to persons skilled in the art.
  • more than one amplification method is used, such as reverse transcription followed by real time quantitative PCR (qRT-PCR).
  • qRT-PCR real time quantitative PCR
  • a set of primers is used for each target sequence.
  • the lengths of the primers depends on many factors, including, but not limited to, the desired hybridization temperature between the primers, the target nucleic acid sequence, and the complexity of the different target nucleic acid sequences to be amplified.
  • a primer is about 15 to about 35 nucleotides in length. In other embodiments, a primer is equal to or fewer than 15, 20, 25, 30, or 35 nucleotides in length. In additional embodiments, a primer is at least 35 nucleotides in length.
  • a forward primer can comprise at least one sequence that anneals to a miRNA and alternatively can comprise an additional 5' non-complementary region.
  • a reverse primer can be designed to anneal to the complement of a reverse transcribed miRNA.
  • the reverse primer may be independent of the miRNA sequence, and multiple miRNA biomarkers may be amplified using the same reverse primer.
  • a reverse primer may be specific for a miRNA biomarker.
  • the qRT-PCR reaction may further be combined with the reverse transcription reaction by including both a reverse transcriptase and a DNA-based thermostable DNA polymerase.
  • a "hot start” approach may be used to maximize assay performance ( U.S. Pat. Nos. 5,411,876 and 5,985,619 ).
  • the components for a reverse transcriptase reaction and a PCR reaction may be sequestered using one or more thermoactivation methods or chemical alteration to improve polymerization efficiency ( U.S. Pat. Nos. 5,550,044 , 5,413,924 , and 6,403,341 ).
  • labels, dyes, or labeled probes and/or primers are used to detect amplified or unamplified miRNAs.
  • detection methods are appropriate based on the sensitivity of the detection method and the abundance of the target.
  • amplification may or may not be required prior to detection.
  • miRNA amplification is preferred.
  • a probe or primer may include Watson-Crick bases or modified bases.
  • Modified bases include, but are not limited to, the AEGIS bases (from Eragen Biosciences), which have been described, e.g., in U.S. Pat. Nos. 5,432,272 , 5,965,364 , and 6,001,983 .
  • bases are joined by a natural phosphodiester bond or a different chemical linkage.
  • Different chemical linkages include, but are not limited to, a peptide bond or a Locked Nucleic Acid (LNA) linkage, which is described, e.g., in U.S. Pat. No. 7,060,809 .
  • LNA Locked Nucleic Acid
  • oligonucleotide probes or primers present in an amplification reaction are suitable for monitoring the amount of amplification product produced as a function of time.
  • probes having different single stranded versus double stranded character are used to detect the nucleic acid.
  • Probes include, but are not limited to, the 5'-exonuclease assay (e.g., TaqManTM) probes (see U.S. Pat. No. 5,538,848 ), stem-loop molecular beacons (see, e.g., U.S. Pat. Nos.
  • stemless or linear beacons see, e.g., WO 9921881 , U.S. Pat. Nos. 6,485,901 and 6,649,349 ), peptide nucleic acid (PNA) Molecular Beacons (see, e.g., U.S. Pat. Nos. 6,355,421 and 6,593,091 ), linear PNA beacons (see, e.g. U.S. Pat. No. 6,329,144 ), non-FRET probes (see, e.g., U.S. Pat. No. 6,150,097 ), SunriseTM/AmplifluorBTM probes (see, e.g., U.S. Pat. No.
  • one or more of the primers in an amplification reaction includes a label.
  • different probes or primers comprise detectable labels that are distinguishable from one another.
  • a nucleic acid, such as the probe or primer may be labeled with two or more distinguishable labels.
  • the concentration of the miRNA is measured using a microarray or another support.
  • a "microarray” is a linear or two-dimensional or three dimensional (and solid phase) array of discrete regions, each having a defined area, formed on the surface of a solid support such as, but not limited to, glass, plastic, or synthetic membrane.
  • the density of the discrete regions on a microarray is determined by the total numbers of immobilized polynucleotides to be detected on the surface of a single solid phase support, such as of at least about 50/cm 2 , at least about 100/cm 2 , or at least about 500/cm 2 , up to about 1,000/cm 2 or higher.
  • the arrays may contain less than about 500, about 1000, about 1500, about 2000, about 2500, about 3000, or more immobilized polynucleotides in total.
  • a DNA microarray is an array of oligonucleotide or polynucleotide probes placed on a chip or other surfaces used to hybridize to amplified or cloned polynucleotides from a sample. Since the position of each particular group of probes in the array is known, the identities of a sample polynucleotides can be determined based on their binding to a particular position in the microarray.
  • an array of any size on a support may be used in the practice of the disclosure, including an arrangement of one or more position of a two-dimensional or three-dimensional arrangement to detect expression of an miRNA.
  • a label is attached to one or more probes and has one or more of the following properties: (i) provides a detectable signal; (ii) interacts with a second label to modify the detectable signal provided by the second label, e.g., FRET (Fluorescent Resonance Energy Transfer); (iii) stabilizes hybridization, e.g., duplex formation; and (iv) provides a member of a binding complex or affinity set, e.g., affinity, antibody-antigen, ionic complexes, hapten-ligand (e.g., biotin-avidin).
  • use of labels can be accomplished using any one of a large number of known techniques employing known labels, linkages, linking groups, reagents, reaction conditions, and analysis and purification methods.
  • MiRNAs can be detected by direct or indirect methods.
  • a direct detection method one or more miRNAs are detected by a detectable label that is linked to a nucleic acid molecule.
  • the miRNAs may be labeled prior to binding to the probe. Therefore, binding is detected by screening for the labeled miRNA that is bound to the probe.
  • the probe is optionally linked to a bead in the reaction volume.
  • nucleic acids are detected by direct binding with a labeled probe, and the probe is subsequently detected.
  • the nucleic acids such as amplified miRNAs, are detected using FIexMAP Microspheres (Luminex) conjugated with probes to capture the desired nucleic acids.
  • FIexMAP Microspheres Luminex
  • Some methods may involve detection with polynucleotide probes modified with fluorescent labels or branched DNA (bDNA) detection, for example.
  • nucleic acids are detected by indirect detection methods.
  • a biotinylated probe may be combined with a streptavidin-conjugated dye to detect the bound nucleic acid.
  • the streptavidin molecule binds a biotin label on amplified miRNA, and the bound miRNA is detected by detecting the dye molecule attached to the streptavidin molecule.
  • the streptavidin-conjugated dye molecule comprises Phycolink® Streptavidin R-Phycoerythrin (PROzyme). Other conjugated dye molecules are known to persons skilled in the art.
  • Labels include, but are not limited to: light-emitting, light-scattering, and light-absorbing compounds which generate or quench a detectable fluorescent, chemiluminescent, or bioluminescent signal (see, e.g., Kricka, L., Nonisotopic DNA Probe Techniques, Academic Press, San Diego (1992 ) and Garman A., Non-Radioactive Labeling, Academic Press (1997 )).
  • Fluorescent reporter dyes useful as labels include, but are not limited to, fluoresceins (see, e.g., U.S. Pat. Nos. 5,188,934 , 6,008,379 , and 6,020,481 ), rhodamines (see, e.g., U.S. Pat.
  • fluorescein dyes include, but are not limited to, 6-carboxyfluorescein; 2',4',1,4,-tetrachlorofluorescein; and 2',4',5',7',1,4-hexachlorofluorescein.
  • the fluorescent label is selected from SYBR-Green, 6-carboxyfluorescein ("FAM”), TET, ROX, VICTM, and JOE.
  • FAM 6-carboxyfluorescein
  • TET 6-carboxyfluorescein
  • ROX ROX
  • VICTM VICTM
  • JOE JOE
  • labels are different fluorophores capable of emitting light at different, spectrally-resolvable wavelengths (e.g., 4-differently colored fluorophores); certain such labeled probes are known in the art and described above, and in U.S. Pat. No.
  • a dual labeled fluorescent probe that includes a reporter fluorophore and a quencher fluorophore is used in some embodiments. It will be appreciated that pairs of fluorophores are chosen that have distinct emission spectra so that they can be easily distinguished.
  • labels are hybridization-stabilizing moieties which serve to enhance, stabilize, or influence hybridization of duplexes, e.g., intercalators and intercalating dyes (including, but not limited to, ethidium bromide and SYBR-Green), minor-groove binders, and cross-linking functional groups (see, e.g., Blackburn et al., eds. "DNA and RNA Structure” in Nucleic Acids in Chemistry and Biology (1996 )).
  • intercalators and intercalating dyes including, but not limited to, ethidium bromide and SYBR-Green
  • minor-groove binders include, but not limited to, ethidium bromide and SYBR-Green
  • cross-linking functional groups see, e.g., Blackburn et al., eds. "DNA and RNA Structure” in Nucleic Acids in Chemistry and Biology (1996 )).
  • methods relying on hybridization and/or ligation to quantify miRNAs may be used, including oligonucleotide ligation (OLA) methods and methods that allow a distinguishable probe that hybridizes to the target nucleic acid sequence to be separated from an unbound probe.
  • OLA oligonucleotide ligation
  • HARP-like probes as disclosed in U.S. Publication No. 2006/0078894 may be used to measure the quantity of miRNAs.
  • a probe ligation reaction may be used to quantify miRNAs.
  • MLPA Multiplex Ligation-dependent Probe Amplification
  • pairs of probes which hybridize immediately adjacent to each other on the target nucleic acid are ligated to each other only in the presence of the target nucleic acid.
  • MLPA probes have flanking PCR primer binding sites. MLPA probes can only be amplified if they have been ligated, thus allowing for detection and quantification of miRNA biomarkers.
  • hemolysis is determined in the biological sample and the sample is not subjected to the method if hemolysis is determined.
  • Hemolysis can be determined in the subject samples by any means known in the art.
  • hemolysis is determined spectrophotometrically, e.g., by measuring the absorbance at different wavelengths (414nm, 541nm, 576nm) to identify the presence and amount of free hemoglobin in the sample (Kirschner et al., 2011).
  • hemolysis is determined by analyzing expression levels of hemolysis-related miRNAs that are upregulated in hemolyzed samples.
  • any of the miRNAs miR-451, miR-486-5p, miR-16, miR-92a or miR-140-3p, which are significantly upregulated in hemolysed samples vs. non-hemolysed samples, are utilized.
  • the hemolysis-related miRNAs are miR-451, miR-486-5p, miR-16, and miR-92a.
  • expression levels of a plurality of normalizing miRNAs that are not upregulated in hemolysed samples are determined, and used to normalize the expression levels of the hemolysis-related miRNAs.
  • These normalizing miRNAs can be used in ratios with hemolysis-related miRNAs to normalize the determined expression levels of the latter miRNAs.
  • the normalizing miRNAs comprise miR-126, miR-15b, miR-221 and miR-30b.
  • hemolysis is further determined by:
  • the cut-off value of this hemolysis assay depends on the control population, e.g., the cut-off where a plurality of unhemolyzed serum samples are used as the control samples will be different than the cut-off where a plurality of hemolyzed serum samples are used as the control samples. See Examples. Additionally, the cut-off can be adjusted, e.g., to achieve desired SE, SP, PPV and NPV values. In some embodiments where unhemolyzed serum samples are used as the control samples the cut-off will be the average (mean or median) ratio of the plurality of control samples. Optionally, this cut-off will have a +/- proportion of a standard deviation to account for differences in variability among the samples used to determine the cut-off value.
  • any of the hemolysis assays using miRNA expression levels described above is also combined with another hemolysis assay, for example the spectrophotometric assay described in Kirschner et al., 2011.
  • LDCT low-dose computed tomography
  • LDCT screening Health care costs of LDCT screening and associated follow-up procedures are significant.
  • Complementing LDCT screening with a non-invasive biomarker test, by reducing down-stream costs, might increase the number of individuals enrolled in LDCT screening ( Peres, J Natl Cancer Inst 105:1-2,2013 ).
  • any of the above-described diagnostic or prognostic methods can be combined with a screening of the subject for lung cancer using a system that does not comprise analysis of miRNA expression.
  • the system may be used prior to, concurrently, or after the miRNA expression analysis. Any system now known or later discovered would be expected to benefit from additional analysis with MSC.
  • Non-limiting examples of such systems include a blood test, an x-ray, computed tomography, positron emission tomography, thoracentesis, bronchoscopy, fine-needle aspiration, thoracoscopy, thoracotomy, or mediastinoscopy.
  • the system is low-dose computed tomography (LDCT).
  • any of the above methods can be used for monitoring the subject for presence of lung cancer and/or risk of developing lung cancer.
  • a subject is monitored when any of the above methods are performed on at least two different biological samples that were taken from the subject at different times.
  • at least one of the at least two different biological samples is taken from the subject after the subject has been treated for lung cancer. Such monitoring evaluates recurrence or risk of recurrence of the lung cancer.
  • the term "treat” is meant to describe administering an agent to eliminate or reduce in severity a sign or symptom of lung cancer.
  • a disorder which can occur in multiple locations is treated if therapy is applied to that disorder in at least one of multiple locations.
  • the above methods can be utilized to select treatment options is where the subject is not treated for lung cancer if a negative presence or risk is determined, or if a low risk is determined in the combined method for predicting the risk of developing or having a tumor.
  • a subject is treated for lung cancer if a positive presence or risk is determined, or if an intermediate or high risk in the combined method is determined.
  • a method of establishing lung cancer treatment options for a subject comprises testing the subject using of the diagnostic and/or prognostic methods described above, and determining treatment options according to the results of the method.
  • the method may further comprise administering a treatment to the subject in need thereof.
  • 24 miRNAs may compose the signature of Presence of a Pulmonary Tumor (PD), the signature of Presence of an Aggressive Pulmonary Tumor (PAD), the signature of Risk of manifesting a Pulmonary Tumor (RD), and the signature of Risk of manifesting an Aggressive Pulmonary Tumor (RAD).
  • Table 1 recites those 24 miRNAs which may be present in each signature.
  • Table 2 provides a summary of the miRNA for use in all aspects of the present invention.
  • Table 2 miRNA Name Sequence hsa-miR-7-2 (pre-miR) hsa-miR-7-2-5p (mature miR 5' arm) UGGAAGACUAGUGAUUUUGUUGU (SEQ ID NO:2) hsa-miR-7-2-3p (mature miR 3' arm) CAACAAAUCCCAGUCUACCUAA (SEQ ID NO:3) hsa-miR-15b (pre-miR) hsa-miR-15b-5p (mature miR 5'arm) UAGCAGCACAUCAUGGUUUACA (SEQ ID NO:5) hsa-miR-15b-3p (mature miR 3'arm) CGAAUCAUUAUUUGCUGCUCUA (SEQ ID NO:6) hsa-miR-16-1 (pre-miR from Chr.13) hsa-miR
  • hsa-miR-19b-1-5p (mature miR 5'arm from Chr. 13) AGUUUUGCAGGUUUGCAUCCAGC (SEQ ID NO:15) hsa-miR-19b-2 (pre-miR from Chr. X) hsa-miR-19b-2-5p (mature miR 5' arm from Chr. X) AGUUUUGCAGGUUUGCAUUUCA (SEQ ID NO:17) hsa-miR-19b-3p (mature miR 3' arm from Chr.
  • hsa-miR-30c-1-3p (mature miR 3' arm from Chr. 1) CUGGGAGAGGGUUGUUUACUCC (SEQ ID NO:32) hsa-miR-30c-2 (pre-miR from Chr. 6) hsa-miR-30c-5p (mature miR 5' arm from Chr. 1 or 6) UGUAAACAUCCUACACUCUCAGC (SEQ ID NO:34) hsa-miR-30c-2-3p (mature miR 3' arm from Chr.
  • hsa-miR-320b-2 pre-miR from Chr. 1:224444706-224444843
  • hsa-miR-320b mature miR from Chr. 1
  • AAAAGCUGGGUUGAGAGGGCAA SEQ ID NO:97
  • hsa-miR-320c-1 pre-miR from Chr. 18:19263471-19263558
  • hsa-miR-320c-2 pre-miR from Chr.
  • hsa-miR-320-c (mature miR from either Chr 18 loci) AAAAGCUGGGUUGAGAGGGU (SEQ ID NO:100)
  • hsa-miR-320d-1 pre-miR from Chr. 13
  • hsa-miR-320d-2 pre-miR from Chr.
  • hsa-miR-320d mature miR from Chr.
  • AAAAGCUGGGUUGAGAGGA (SEQ ID NO:103) hsa-miR-320e (pre-miR) hsa-miR-320e (mature miR) AAAGCUGGGUUGAGAAGG (SEQ ID NO:105) hsa-miR-324 (pre-miR) hsa-miR-324 (mature miR 5' arm) CGCAUCCCCUAGGGCAUUGGUGU (SEQ ID NO:107) hsa-miR-324 (mature miR 3' arm) ACUGCCCCAGGUGCUGCUGG (SEQ ID NO:108) hsa-miR-429 (pre-miR) hsa-miR-429 (mature miR) UAAUACUGUCUGGUAAAACCGU (SEQ ID NO:110) hsa-miR-451a (pre-miR) hsa-miR-451a (mature miR) AAA
  • the following examples relate to the clinical utility of a plasma-based microRNA signature classifier within computed tomography lung cancer screening, also referred to as the Correlative MILD Trial Study.
  • a plasma-based microRNA signature classifier within computed tomography lung cancer screening
  • MILD randomized Multicentre Italian Lung Detection
  • MILD Multicentre Italian Lung Detection
  • NMV neurodegenerative disease
  • a sample at-diagnosis was available for 50 patients and a pre-disease sample for 19 patients ( FIG. 1 ).
  • the pre-disease samples were collected from 8 to 35 months before lung cancer detection with a median lag time of 18 months.
  • RNA profiling Total RNA was extracted from 200 ⁇ l plasma samples with the mirVana PARISKit (Life Technologies, Ambion) and eluted in 50 ⁇ l of buffer. miRNA expression was determined in 3 ⁇ l of eluted RNA using the Multiplex Pools Protocol on custom-made microfluidics card (Life Technologies, Applied Biosystems) containing the 24 miRNAs spotted on duplicates. For each sample, Ct's of individual miRNAs was determined using ViiA7 software (Life Technologies, Applied Biosystems) with a threshold of 0.15 and an automatic baseline. For input into the MSC, the average of the duplicate readings of pre-defined miRNA ratios was calculated as previously described (Boeri et al., 2011).
  • the SE, SP, PPV and NPV were calculated for the various time intervals from blood sample collection to lung cancer diagnosis (6, 12, 18 and 24 months), using the methodology described by Heagerty et al, Biometrics 56:337-344 (2000 ) and Zheng and Heagerty, Biometrics 63:332-341 (2007 ).
  • Plasma samples with the presence of hemolysis were removed from subsequent analyses because hemolysis of blood cells such as red blood cells (RBC) or platelets releases contaminating miRNAs (Kirschner et al., 2011; Pritchard et al., 2012).
  • Two quality control (QC) measurements were used for this evaluation.
  • QC quality control
  • a second QC step was implemented to obtain even greater sensitivity of hemolysis by analyzing expression levels of hemolysis-related miRNAs contained within the miRNA signature classifier (MSC; mir-451, 486-5p, 16, 92a) for all samples. Plasma samples with expression levels of hemolysis-related miRNAs that exceeded 2 standard deviations from the overall mean of all samples were excluded from subsequent analyses. Samples with detectable spectrophotometrically measured hemolysis were also excluded in this second QC step. No difference in the frequency or in the amount of hemolysis as measured either spectrophotometrically or by hemolysis-related miRNAs analysis was observed in the cancer vs control samples.
  • MSC miRNA signature classifier
  • miRNA differentially expressed in plasma could simply reflect different blood cell counts (Pritchard, 2012).
  • miRNA ratios composed by neutrophil-expressed and RBC-expressed miRNAs were compared with ratios between the levels of neutrophil and RBC obtained by complete blood count (CBC) from 23 lung cancer patients of this present study.
  • CBC complete blood count
  • none of the miRNA ratios present in the signatures were found to have a significant correlation with respective CBC ratios.
  • Table 3 Plasma miRNA ratios correlation to blood cell counts in 23 lung cancer patients. Pearson correlation coefficients of neutrophil vs. RBC miRNA ratios and neutrophil vs. RBC counts in the 23 samples are shown in the table.
  • the second QC step involving analysis of hemolysis-related miRNAs may additionally or alternatively utilize a hemolysis miRNA signature comprising miRNAs contained within the MSC as described herein.
  • Samples of whole blood were collected, with addition of EDTA, and stored at room temperature for no longer than 1-2 hours before processing. Storage at reduced temperature is to be avoided because it may lead to non-specific release of miRNA.
  • the samples were centrifuged at approximately 1250 times g at 4°C for 10 minutes to separate plasma, which was carefully transferred while avoiding material closest to the lymphocytic ring.
  • the plasma was centrifuged again under the same conditions and then separated into aliquots, with avoidance of pelleted material, that were stored at -80 °C for up to 1 year or longer.
  • miRNAs Four miRNAs (miR-16, miR-451, miR-486-5p, and miR-92a) were included in the development of the miRNA signature.
  • Raw Ct values (a measure of expression level) are shown in Table 4.
  • Table 4 Raw Ct values for miRNAs in hemolyzed versus non-hemolyzed samples. NOT HAEMOLYSED HAEMOLYSED Ct average s.d. Ct average s.d.
  • Mean baseline miRNA ratios were calculated using the formula, mean ratio + 1.5 s.d. (standard deviation), from non-hemolyzed plasma samples from 98 disease-free individuals. These baseline ratios were set as the cut-off for each of the 16 miRNA ratios in developing the miRNA signature for hemolysis.
  • the hemolysis miRNA signature can be used to detect hemolysis in plasma samples.
  • Table 6 shows a list of 16 ratios composed of 8 miRNAs (miR-126, 15b, 30b, 221, 451, 16, 486-5p and 92a).
  • the 4 miRNAs, miR-451, miR-486-5p, miR-16 and miR-92a are all overexpressed in hemolyzed samples. This overexpression can be used as an indicator of hemolysis in a plasma sample.
  • the plasma sample is positive for hemolysis. Table 6.
  • miRNA signature for hemolysis Ratios of miRNAs Cut-off (log2) 126/451 ⁇ -0.74 15b/451 ⁇ -4.07 221/451 ⁇ -3.81 30b/451 ⁇ -1.53 126/486 ⁇ 0.34 15b/486 ⁇ -3.33 221/486 ⁇ -2.63 30b/486 ⁇ -0.70 126/92a ⁇ 1.86 15b/92a ⁇ -1.70 221/92a ⁇ -1.08 30b/92a ⁇ 0.83 126/16 ⁇ -1.92 15b/16 ⁇ -5.34 221/16 ⁇ -5.01 30b/16 ⁇ -2.75
  • Hemoglobin is known in the art to have an absorbance wavelength at 414 nm.
  • One standard method used in both scientific and clinical practice to analyze hemolysis is the spectroscopic measurement at the wavelength of 414 nm (using an absorbance threshold of 0.2) of free hemoglobin in plasma samples.
  • the absorbance at 414 nm was normalized against the absorbance at 375 nm in order to overcome the high background signal in some samples (e.g., in lipemic samples).
  • a cut-off of 1.4 for the ratio of absorbance at 414 nm to absorbance at 375 nm was set.
  • samples with a value of A414nm/A375nm greater than 1.40 corresponded to the miRNA signature wherein at least 8 out of 16 miRNA ratios exceeded their respective cut-offs.
  • These settings were used to evaluate the power of the miRNA signature in distinguishing the 24 hemolyzed from 98 non-hemolyzed (based on visual inspection) plasma samples.
  • the miRNA signature method exhibited a sensitivity of 0.88 and a specificity of 0.93. In regard to sensitivity, it was clear that the 24 samples that were visually assessed to be hemolyzed were indeed hemolyzed.
  • the hemolysis miRNA signature and spectrophotometry methods were compared using an independent series composed of a selection of 60 plasma samples that were visually hemolyzed (red, orange or dark yellow) and 43 plasma samples non-hemolyzed based on visual inspection. Concerning sensitivity (Table 7), the 5 most hemolyzed (red) samples were all recognized as positive for hemolysis by both methods. However, in evaluating the orange and dark yellow samples, the miRNA signature method was more sensitive (>90% versus 76% for the spectrophotometric method). Table 7. Comparing spectrophotometer and miRNAs results to evaluate hemolysis in 60 visually hemolyzed plasma samples.
  • MSC MiRNA signatures classifier
  • the training set was also used to establish the minimum number of ratios exceeding the respective cut-off value needed to be considered positive: 10/27 for RD, 9/27 for PD, 14/28 for RAD, 14/28 for PAD.
  • the three-level MSC was then defined as follows: Low risk (L) if RD neg ⁇ PD neg ⁇ RAD neg ⁇ PAD neg ; Intermediate risk (I) if RD pos U PD pos ⁇ RAD neg ⁇ PAD neg ; or High risk (H) if RAD pos U PAD pos .
  • median time from randomization to diagnosis was 29 months (range 1-82), and median time from plasma sampling to diagnosis was 2 months (range 0-35).
  • median time from randomization to plasma sampling was 44 months (range 0-58) and median time from plasma sampling to last follow-up was 27 months (range 3-41).
  • MSC risk groups were examined for all 939 subjects according to lung cancer occurrence, lung cancer death, and tumor stage (Table 11). MSC Intermediate and High correctly classified 60 of 69 lung cancer patients with 87% SE, 81% SP, 27% PPV and 99% NPV. Of the 19 lung cancer patients that died during follow-up, 18 were positive at the MSC test, with 95% SE, 81% SP, 10% PPV and 100% NPV. No deaths due to causes other than lung cancer were observed during the follow-up.
  • Comparative diagnostic performance of MSC for lung cancer detection within the two arms was similar with 88% SE, 80% SP, 31% PPV, 99% NPV and 82% SE, 83% SP, 16% PPV, 99% NPV for LDCT and Observational arms respectively.
  • Table 11 Distribution of 69 subjects with lung cancer and 870 subjects without lung cancer according to lung cancer prevalence, lung cancer death, and lung cancer stage and miRNA signature classifier (MSC), with corresponding sensitivity (SE), specificity (SP), positive predictive value (PPV), and negative predictive value (NPV).
  • SE sensitivity
  • SP specificity
  • PPV positive predictive value
  • NPV negative predictive value
  • Example 3 Complementary diagnostic performance of LDCT and MSC
  • LDCT Restricting the analysis to the total of 652 subjects in the LDCT arm, LDCT identified 46 of 58 lung cancer subjects missing 3 patients within the 251 subjects with no pulmonary nodule detected and 9 patients because of an interval cancer for a SE of 79% (Table 13).
  • the three cancers with "no pulmonary nodule" comprised of one non-solid lesion, one mediastinal adenopathy, and one pleural effusion.
  • Pre-specified binary risk groups of MSC (considering High and Intermediate versus Low) identified 40 of 46 LDCT-detected cancers, 8 of 9 interval cancers and all 3 subjects with "no pulmonary nodule”. Table 13.
  • MSC miRNA signature classifier
  • LDCT low-dose computed tomography
  • MILD Multicentric Italian Lung Detection
  • LDCT had a SP of 81% for the clinically actionable subgroup of non-calcified nodules >5 mm and an associated false positive rate of 19.4% (115/594) (Table 13).
  • LDCT and MSC double-positive subjects were considered, the false positive rate decreased to 3.7% (22/594), with a decrease in SE (40/58, 69%).
  • LDCT or MSC considering as positive a subject with at least one positive test (LDCT or MSC), the combined use of LDCT and MSC identified 57 of 58 cases, with a SE of 98% and a SP of 65%.
  • MSC detected 9 of 11 (82%) lung cancers that occurred in the observational arm (Table 13).
  • the diagnostic characteristic of high sensitivity coupled with a NPV of 99% indicates that MSC is a clinically validated screening test. Moreover, the diagnostic performance of MSC as a predictor of lung cancer development was confirmed by the time dependency analysis.
  • MSC identified subjects with a high likelihood of death-by-disease.
  • MSC had a SE of 95% and NPV of 100% for death-by-disease for 939 subjects across both arms.
  • the MSC risk groups were associated with significantly different survival at 3 years for the entire cohort of 939 subjects (100%, 97% and 77% for Low, Intermediate and High MSC respectively).
  • MSC could complement LDCT screening by reducing false-positive results and enable greater standardization of diagnostic algorithms, thereby decreasing health care costs.
  • further repetitions of MSC rather than LDCT could be proposed for individuals with a Low MSC, given the absence of mortality at three years for Low MSC subjects.
  • the present blinded study of a pre-specified plasma-based assay represents the largest study testing a biomarker within a LDCT screening trial, and demonstrates the superior diagnostic performance of LDCT if combined with MSC.

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